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LOC121627905 Sharpr-MPRA regulatory region 7536 [ Homo sapiens (human) ]

Gene ID: 121627905, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627905
Gene description
Sharpr-MPRA regulatory region 7536
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121627905 in Genome Data Viewer
Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (34129703..34129997)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (35856080..35856374)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (32717509..32717803)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 2 subunit beta Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32698990-32699652 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32699653-32700314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12832 Neighboring gene ribosomal protein S2 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32731215-32731715 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:32741705-32742632 Neighboring gene agouti signaling protein Neighboring gene NANOG hESC enhancer GRCh37_chr20:32819632-32820133 Neighboring gene exportin for tRNA pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17757 Neighboring gene NANOG hESC enhancer GRCh37_chr20:32830321-32830822 Neighboring gene adenosylhomocysteinase Neighboring gene DENR pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_075096.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    34129703..34129997
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    35856080..35856374
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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